Normally, I would just map the reads with the flag "maxindel=100k" (or whatever is appropriate, given the length of the genome) and then call variants with "callvariants.sh" using the flag "rarity=0.01" to find low-frequency events. But alternatively, you can separate the reads with multiple BBMap passes, like this:
bbmap.sh in=reads.fq outm=mapped.fq maxindel=100k
bbmap.sh in=mapped.fq outm=normal.fq outu=longdeletion.fq maxindel=100k dellenfilter=20
bbmap.sh in=longdeletion.fq out=mapped_longdeletion.sam maxindel=100k